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Job review #1473


Job #1473 review - http://beta.mole.upol.cz/online/1473/

Generated on 2025-01-30 04:35:40 by service v.

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Structure: 1tqn (structure summary on pdb.org)
Unit: 1
Chain: 1
Identify tunnels starting from multiple cavities. This can provide a good initial insight into the tunnel structure of the protein.
: clear
Example: GLU 308, THR 309
The starting point is defined as a center of mass of selected residues. You can choose residues using by the sequence inspector below the Jmol window. In case you analyze an enzyme structure, MOLEOnline offers an active site residues (from the Catalytic Site Atlas, if available) as the starting point.
Active sites from CSA:
A GLU 308, A THR 309
A THR 309, A PHE 435, A CYS 442
:
Ignoring coordinates with HETATM records for non-polymer or other “non-standard” chemical coordinates, such as atoms presented in HET groups (ligands, prosthetic groups) in PDB format. Reminder: water molecules (WAT, HOH, SOL) are ignored everytime in MOLEonline 2.0!

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:
Example: A GLU 308, B THR 309.
List of residues to be ignored prior computation of channel.
Starting point [X,Y,Z]: clear
Specify starting point as an X, Y, Z coordinates (as decimal numbers in Å).
Ending point [X,Y,Z]: clear
Specify ending point as an X, Y, Z coordinates (as decimal numbers in Å).
:
Radius used for construction of molecular surface.
:
Lower bound of the tunnel radius.
:
Determines the density of tunnel exits on the molecular surface.
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Better starting points are localized within the defined radius from the original starting point.
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Tunnels with bottleneck bellow this radius will be removed.
:
Used to remove tunnels based on their percentage similarity.

reset to default values